Hi Mark,
You stated at the beginning of this thread that you had the fuel squirt turned down to 2 seconds. Does that mean that you have increased the AP timing gap (see my gallery page 4 for a picture) to achieve this? If this is true this is where you problem is coming from.
The AP timing is critical for those times when you whack the throttle open. The standard adjustment is .100". An alternative method for the bigger motors like ours is to set the slide opening to 1.25mm's, and then set the AP pump rod so that it has no play in it, without depressing the AP diaphragm. The .100" gap is much easier and you don't have to take the carb off the bike! When you bought your quick shot there should have been a little piece of thick construction paper to be used for setting the AP gap, did you use that to set the gap?
The trick is to get the AP to start it's squirt just as the slide is opened but not hit the back of the slide.
There are a couple of ways to limit the squirt to 1 or 2 seconds. One is the BK mod (just do a google search and you'll find it) which requires one to drill the flange of the carb where the dust cover goes and then put a limiting bolt, or stop that goes up to the black AP arm wherein you can adjust the throw of the arm or duration without affecting the initial timing.
The other is to buy a honda diaphragm described in buzzards "$40 FCR spruce up". This will limit squirt time to about 1 second. And is the best method I have found so far in limiting squirt duration, while maintaining correct squirt timing.
If you delay the start of the AP squirt too much you will end up with a lean bog. I have been testing this for some time now to solve a rich stutter problem when just opening the throttle when the motor is good and hot, and found that increasing the gap in 1/4 turn increments did eliminate the rich stutter. However, once the rich stutter was eliminated, there would be a slight hesitation because the fuel squirt was delayed too much. This was anything beyond 1/2 turn, or anything exceeding .115" of gap.
You don't indicate what needle you are using in your post, but, position #2 sounds a bit lean to me if my hunch on which needle you are running is correct, even at 4500'. Please let us know which needle you are using. An easy way to get rid of a an off idle bog when whacking the throttle open is to raise the needle, or lower the clip however you want to phrase it.
You also say that you are using a 45 pilot @ two turns out, correct?
Have you checked your float level lately? Just asking to be sure that all settings are correct so we don't go chasing our tails. Another reason I'm asking this is b/c of your description of the conditions in which it bogs. You say it does it when you land in 3rd and pin it, and you also say that it bogs on the face of the jump. There is an incredible amount of centrifugal force pushing down on everything when you land, and go up the face of a double. This of course has en effect on the fuel in the bowl. That trick little float bowl you are looking at by R&D is $250 bucks, and has an adjustable leak jet. I had thought about buying one myself but have solved my problems without one. But then again I'm not doing the kind of stuff you are either. However, I do ride some pretty gnarly terrain in my desert races and have some pretty severe landings and huge whoop sections and do not experience this kind of bog.
Hope this helps,